Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/immicro/CAL_BUDGET.json +1017 -0
- paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/BUILD.json +71 -0
- paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/CAL_BUDGET.json +989 -0
- paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold4/alpha_n5.npy +3 -0
paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/immicro/CAL_BUDGET.json
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"DB2": 8,
|
| 1005 |
+
"DB6": 8,
|
| 1006 |
+
"DB7": 7,
|
| 1007 |
+
"DB3": 6,
|
| 1008 |
+
"DB4": 5,
|
| 1009 |
+
"DB1": 4
|
| 1010 |
+
},
|
| 1011 |
+
"alpha_genes_estimated": 10778,
|
| 1012 |
+
"alpha_genes_estimated_all_training": 10797
|
| 1013 |
+
}
|
| 1014 |
+
}
|
| 1015 |
+
}
|
| 1016 |
+
}
|
| 1017 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/BUILD.json
ADDED
|
@@ -0,0 +1,71 @@
|
|
|
|
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|
|
|
|
|
|
|
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|
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|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"written_utc": "2026-10-01T01:45:18.478120+00:00",
|
| 3 |
+
"script": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/build_sex_gene_list.py",
|
| 4 |
+
"script_sha256": "8637485d77bd6b85ae65423f59f7904dac0a3dfe3defcecaf13e49ab10e7724f",
|
| 5 |
+
"inputs": {
|
| 6 |
+
"/home/sj_server_1/gblee/ablations_data_repro_20260802/fixed_assets/gencode.v50.annotation.gtf.gz": "83fba3e9b03f0b8c958f3595c6c350adc55f468abf8b0e47b6d5284cfe13a453",
|
| 7 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sources/Tukiainen2017_Suppl.Table.13.xlsx": "eb7d466f2660c19bc5d51181096e080d927d5e6fb7c216a564ced174a3a864b7",
|
| 8 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sources/GCF_000001405.40_GRCh38.p14_assembly_regions.txt": "8e6faeaaea86e1efd6c38299a698cda76d05ee092701526e5457d38fa27783f6"
|
| 9 |
+
},
|
| 10 |
+
"axis": {
|
| 11 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/features.npz gene_ids (identical in 5 cohorts)",
|
| 12 |
+
"n_genes": 20097,
|
| 13 |
+
"n_chrX": 867,
|
| 14 |
+
"n_chrY": 61
|
| 15 |
+
},
|
| 16 |
+
"par_regions": [
|
| 17 |
+
{
|
| 18 |
+
"region": "PAR#1",
|
| 19 |
+
"chromosome": "chrX",
|
| 20 |
+
"start": 10001,
|
| 21 |
+
"end": 2781479
|
| 22 |
+
},
|
| 23 |
+
{
|
| 24 |
+
"region": "PAR#2",
|
| 25 |
+
"chromosome": "chrX",
|
| 26 |
+
"start": 155701383,
|
| 27 |
+
"end": 156030895
|
| 28 |
+
},
|
| 29 |
+
{
|
| 30 |
+
"region": "PAR#1",
|
| 31 |
+
"chromosome": "chrY",
|
| 32 |
+
"start": 10001,
|
| 33 |
+
"end": 2781479
|
| 34 |
+
},
|
| 35 |
+
{
|
| 36 |
+
"region": "PAR#2",
|
| 37 |
+
"chromosome": "chrY",
|
| 38 |
+
"start": 56887903,
|
| 39 |
+
"end": 57217415
|
| 40 |
+
}
|
| 41 |
+
],
|
| 42 |
+
"counts": {
|
| 43 |
+
"chrY_on_axis": 61,
|
| 44 |
+
"chrY_PAR_kept": 18,
|
| 45 |
+
"chrY_nonPAR_excluded": 43,
|
| 46 |
+
"tukiainen_rows_selected": 178,
|
| 47 |
+
"tukiainen_selected_by_status": {
|
| 48 |
+
"Variable": 89,
|
| 49 |
+
"Escape": 82,
|
| 50 |
+
"Inactive": 6,
|
| 51 |
+
"Unknown": 1
|
| 52 |
+
},
|
| 53 |
+
"tukiainen_new_calls": 7,
|
| 54 |
+
"tukiainen_not_on_axis": 10,
|
| 55 |
+
"tukiainen_PAR_kept": 15,
|
| 56 |
+
"chrX_escape_excluded": 153,
|
| 57 |
+
"chrX_escape_by_reason": {
|
| 58 |
+
"chrX XCI escape (Tukiainen 2017: Variable)": 85,
|
| 59 |
+
"chrX XCI escape (Tukiainen 2017: Escape)": 62,
|
| 60 |
+
"chrX XCI escape (Tukiainen 2017: new call)": 6
|
| 61 |
+
},
|
| 62 |
+
"mapped_by_symbol": 1,
|
| 63 |
+
"par_status_disagrees_with_tukiainen_region": [],
|
| 64 |
+
"axis_genes_crossing_a_PAR_boundary": [
|
| 65 |
+
"XG",
|
| 66 |
+
"TMLHE",
|
| 67 |
+
"SPRY3"
|
| 68 |
+
],
|
| 69 |
+
"total_excluded": 196
|
| 70 |
+
}
|
| 71 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/CAL_BUDGET.json
ADDED
|
@@ -0,0 +1,989 @@
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|
| 1 |
+
{
|
| 2 |
+
"schema": "pbisc_sdd.ft_intradataset.cal_budget.v1",
|
| 3 |
+
"dataset": "ye2026_sepsis",
|
| 4 |
+
"written_utc": "2026-10-01T01:45:06.066177+00:00",
|
| 5 |
+
"rule": "alpha fitted on runs/<ds>/fold<k>/lora_n<n>/RUN.json train_rows + inner_val_rows; applied to the fold's test rows (prepare_dataset.py arithmetic)",
|
| 6 |
+
"cells_per_bulk": 1500,
|
| 7 |
+
"features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
|
| 8 |
+
"builder": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/realbulk_generation_20260922/build_realbulk_conditions.py",
|
| 9 |
+
"builder_sha256": "e818d69e6801b5699579db7fc450590a266708d1fc2d544743e8624c9ee6a30a",
|
| 10 |
+
"folds": {
|
| 11 |
+
"0": {
|
| 12 |
+
"test_rows": 17,
|
| 13 |
+
"reproduces_test_cal": true,
|
| 14 |
+
"n": {
|
| 15 |
+
"5": {
|
| 16 |
+
"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_cal_n5.npz",
|
| 17 |
+
"sha256": "653dac92506f0a1bcbcb2de77013a7b16a9bf58105f70137fd29b6a804c1a937",
|
| 18 |
+
"state": "written",
|
| 19 |
+
"lora_run": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_n5/RUN.json",
|
| 20 |
+
"lora_checkpoint_sha256": "a65c53eaa787ea2da22690aad530386869a3d8125e6cbe8ad0b000abb334b8cd",
|
| 21 |
+
"fit_sample_ids": [
|
| 22 |
+
"Abd-S120",
|
| 23 |
+
"HC16",
|
| 24 |
+
"IC10",
|
| 25 |
+
"IC19",
|
| 26 |
+
"Res-PS26",
|
| 27 |
+
"Res-S10",
|
| 28 |
+
"Res-S127",
|
| 29 |
+
"Res-S136",
|
| 30 |
+
"Res-S146",
|
| 31 |
+
"Res-S166",
|
| 32 |
+
"Res-S19",
|
| 33 |
+
"Skin-S43"
|
| 34 |
+
],
|
| 35 |
+
"n_fit_rows": 12,
|
| 36 |
+
"n_train_rows": 5,
|
| 37 |
+
"n_inner_val_rows": 7,
|
| 38 |
+
"fit_groups": {
|
| 39 |
+
"adult_sepsis": 8,
|
| 40 |
+
"adult_ICU_ctrl": 2,
|
| 41 |
+
"adult_HC": 1,
|
| 42 |
+
"ped_sepsis": 1
|
| 43 |
+
},
|
| 44 |
+
"alpha_genes_estimated": 11572,
|
| 45 |
+
"alpha_genes_estimated_all_training": 11592
|
| 46 |
+
},
|
| 47 |
+
"10": {
|
| 48 |
+
"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_cal_n10.npz",
|
| 49 |
+
"sha256": "4e1de80d49c9399283300e6d48fe581202135acf46221f825bf2f19fe9e74654",
|
| 50 |
+
"state": "written",
|
| 51 |
+
"lora_run": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_n10/RUN.json",
|
| 52 |
+
"lora_checkpoint_sha256": "64862c722d8c25eeb36bbfc80925da4bbaff6a70d3272a4d0cad598208540965",
|
| 53 |
+
"fit_sample_ids": [
|
| 54 |
+
"Abd-PS20",
|
| 55 |
+
"Abd-S120",
|
| 56 |
+
"Abd-S42",
|
| 57 |
+
"HC16",
|
| 58 |
+
"IC10",
|
| 59 |
+
"IC19",
|
| 60 |
+
"PHC05",
|
| 61 |
+
"Res-PS26",
|
| 62 |
+
"Res-S10",
|
| 63 |
+
"Res-S127",
|
| 64 |
+
"Res-S136",
|
| 65 |
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"Res-S146",
|
| 66 |
+
"Res-S166",
|
| 67 |
+
"Res-S174",
|
| 68 |
+
"Res-S184",
|
| 69 |
+
"Res-S19",
|
| 70 |
+
"Skin-S43"
|
| 71 |
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],
|
| 72 |
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"n_fit_rows": 17,
|
| 73 |
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"n_train_rows": 10,
|
| 74 |
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"n_inner_val_rows": 7,
|
| 75 |
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"fit_groups": {
|
| 76 |
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"adult_sepsis": 11,
|
| 77 |
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"ped_sepsis": 2,
|
| 78 |
+
"adult_ICU_ctrl": 2,
|
| 79 |
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"adult_HC": 1,
|
| 80 |
+
"ped_HC": 1
|
| 81 |
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},
|
| 82 |
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"alpha_genes_estimated": 11564,
|
| 83 |
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"alpha_genes_estimated_all_training": 11592
|
| 84 |
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},
|
| 85 |
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"20": {
|
| 86 |
+
"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_cal_n20.npz",
|
| 87 |
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"sha256": "a88e3b6a243dae4fa9a304ac05e9055235d819cd3c3351f2666d66cd5d7c75c3",
|
| 88 |
+
"state": "written",
|
| 89 |
+
"lora_run": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_n20/RUN.json",
|
| 90 |
+
"lora_checkpoint_sha256": "490df820aab33840dc0bd940d88f005452fa8788bdc39fa12c6e45d3336cecb2",
|
| 91 |
+
"fit_sample_ids": [
|
| 92 |
+
"Abd-PS04",
|
| 93 |
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"Abd-PS05",
|
| 94 |
+
"Abd-PS20",
|
| 95 |
+
"Abd-S120",
|
| 96 |
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"Abd-S42",
|
| 97 |
+
"HC16",
|
| 98 |
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"IC10",
|
| 99 |
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"IC16",
|
| 100 |
+
"IC19",
|
| 101 |
+
"PHC05",
|
| 102 |
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"PIC01",
|
| 103 |
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"PIC02",
|
| 104 |
+
"Res-PS26",
|
| 105 |
+
"Res-S10",
|
| 106 |
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"Res-S127",
|
| 107 |
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"Res-S136",
|
| 108 |
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"Res-S146",
|
| 109 |
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"Res-S164",
|
| 110 |
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"Res-S166",
|
| 111 |
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"Res-S174",
|
| 112 |
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"Res-S177",
|
| 113 |
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"Res-S184",
|
| 114 |
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"Res-S19",
|
| 115 |
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"Skin-S142",
|
| 116 |
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"Skin-S43",
|
| 117 |
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"Skin-S74",
|
| 118 |
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"Uri-S20"
|
| 119 |
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|
| 120 |
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"n_fit_rows": 27,
|
| 121 |
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|
| 122 |
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|
| 123 |
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"fit_groups": {
|
| 124 |
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|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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"adult_HC": 1,
|
| 129 |
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|
| 130 |
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},
|
| 131 |
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"alpha_genes_estimated": 11576,
|
| 132 |
+
"alpha_genes_estimated_all_training": 11592
|
| 133 |
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},
|
| 134 |
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"40": {
|
| 135 |
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"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_cal_n40.npz",
|
| 136 |
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"sha256": "8e09fb5affc5028b39bd5d92e7c5eeb6cec86d9e35380f3a13a348e175837bca",
|
| 137 |
+
"state": "written",
|
| 138 |
+
"lora_run": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_n40/RUN.json",
|
| 139 |
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"lora_checkpoint_sha256": "523514d397a70fbcd782677705c175a3cdbf0a0bf0be1f89b45e6d3f17e33061",
|
| 140 |
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"fit_sample_ids": [
|
| 141 |
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"Abd-PS04",
|
| 142 |
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"Abd-PS05",
|
| 143 |
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"Abd-PS07",
|
| 144 |
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"Abd-PS20",
|
| 145 |
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"Abd-PS27",
|
| 146 |
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"Abd-S102",
|
| 147 |
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"Abd-S103",
|
| 148 |
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"Abd-S120",
|
| 149 |
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"Abd-S156",
|
| 150 |
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"Abd-S42",
|
| 151 |
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"Abd-S51",
|
| 152 |
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"Abd-S83",
|
| 153 |
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"HC12",
|
| 154 |
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"HC13",
|
| 155 |
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"HC16",
|
| 156 |
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"IC10",
|
| 157 |
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"IC16",
|
| 158 |
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"IC19",
|
| 159 |
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"IC22",
|
| 160 |
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"PHC02",
|
| 161 |
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"PHC05",
|
| 162 |
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"PIC01",
|
| 163 |
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"PIC02",
|
| 164 |
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"PIC05",
|
| 165 |
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"Res-PS02",
|
| 166 |
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"Res-PS16",
|
| 167 |
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"Res-PS26",
|
| 168 |
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"Res-S10",
|
| 169 |
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|
| 170 |
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|
| 171 |
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|
| 172 |
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|
| 173 |
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paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold4/alpha_n5.npy
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:e8669b2015a63e95b2e2bc0e83e0702503c1628035572540a1d6076274a37c5b
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size 160904
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